The human body—an amazing biological system that scales up fractally from its cellular building blocks—exhibits an incredible ability to self heal. Why then, are chronic diseases and degeneration on the rise in the population? Why are we sicker, more obese, and more depressed and stressed than ever before in human history? Why can’t we heal? The answers to these questions may lie in our ancestry, and modern departure from the human ecological niche. The ability to heal requires proper spatio-temporal inputs—nutrition, sleep, stress, activity, and socialization—in order for cellular signaling to occur properly across semi-permeable cell membranes. We first review key steps in the evolutionary history of multicellular life, focusing on the fundamental role of cell-cell interactions. Next, we present this as an important framework by which to understand how the entrainment of physiological signals in homeostatic mechanisms reveals new insights into the processes of disease. Examples are drawn from the evolution of metabolism, nutrition, and respiration in multicellular life. We argue that disease processes result from a mismatch between the physiological inputs an individual receives and their optimal amount and fractal distribution as determined by an individual’s ancestry. A comparative analysis is a useful tool by which to illuminate deep homologies that reveal a mechanistic account for disease processes. This cell-molecular approach provides a useful contrast to the traditional reductionist approach to disease exemplified by the human genome project. As an example, we describe how cell-cell communication drives the ontogeny and phylogeny of physiology, producing the tissues, organs, and organ systems that hierarchically serve human physiology on various levels. Modern society, with its disconnected and stress-riddled lifestyle, is increasingly failing to provide the proper inputs for healthy gene expression and physiological function. Thus, the answers to our modern health woes—physical, mental, and social—may lie in acknowledging the powerful roles that our past has played in shaping our bodies. Finding ways to provide the proper inputs of the human ecological niche in the modern day may lead to significant, perhaps staggering improvements in our health and wellness. The fractal mathematics underpinning these dynamics also serves as a metaphor for the Ancestral Health Movement, which is currently arising as a multi-cultural, multi-national grass-roots pluralistic phenomenon.